SPARSE: Quadratic Time Simultaneous Alignment and
Folding of RNAs

Synopsis

SPARSE is a tool for the simultaneous alignment and folding of
RNAs; similar to LocARNA, but with improved speed. Its asymptotic time
complexity is equivalent to a sequence alignment algorithm (only
quadratic time). Background on the novel SPARSE algorithm is given in
our publication; complementary, we provide
PDF slides
(from the Benasque RNA meeting
2015.)

For multiple alignment application, sparse inherits mlocarna
progressive alignment approach, therefor one can do a multiple alignment
with sparse by invoking mlocarna and mentioning sparse as the
pairwise aligner tool.